Water in protein hydration and ligand recognition
M Maurer, C Oostenbrink - Journal of Molecular Recognition, 2019 - Wiley Online Library
This review describes selected basics of water in biomolecular recognition. We focus on a
qualitative understanding of the most important physical aspects, how these change in …
qualitative understanding of the most important physical aspects, how these change in …
Water molecules at protein–drug interfaces: computational prediction and analysis methods
The fundamental importance of water molecules at drug–protein interfaces is now widely
recognised and a significant feature in structure-based drug design. Experimental methods …
recognised and a significant feature in structure-based drug design. Experimental methods …
Computational Redesign of an ω-Transaminase from Pseudomonas jessenii for Asymmetric Synthesis of Enantiopure Bulky Amines
Q Meng, C Ramírez-Palacios, N Capra… - ACS …, 2021 - ACS Publications
ω-Transaminases (ω-TA) are attractive biocatalysts for the production of chiral amines from
prochiral ketones via asymmetric synthesis. However, the substrate scope of ω-TAs is …
prochiral ketones via asymmetric synthesis. However, the substrate scope of ω-TAs is …
[HTML][HTML] The role of water in ligand binding
Exploration of the complex modulatory role of water in ligand–target binding is a current
challenge of drug design. This review reports on recent advances of prediction of water …
challenge of drug design. This review reports on recent advances of prediction of water …
The advances and limitations of the determination and applications of water structure in molecular engineering
BZ Zsidó, B Bayarsaikhan, R Börzsei, V Szél… - International Journal of …, 2023 - mdpi.com
Water is a key actor of various processes of nature and, therefore, molecular engineering
has to take the structural and energetic consequences of hydration into account. While the …
has to take the structural and energetic consequences of hydration into account. While the …
Heterogeneous and allosteric role of surface hydration for protein–ligand binding
Atomistic-level understanding of surface hydration mediating protein–protein interactions
and ligand binding has been a challenge due to the dynamic nature of water molecules near …
and ligand binding has been a challenge due to the dynamic nature of water molecules near …
Assessing the predictive power of relative binding free energy calculations for test cases involving displacement of binding site water molecules
Improved sampling methodologies, more accurate force fields, and access to longer
simulation time scales have led to an increased application of Relative Binding Free Energy …
simulation time scales have led to an increased application of Relative Binding Free Energy …
Uncovering water effects in protein–ligand recognition: importance in the second hydration shell and binding kinetics
W Chen, H He, J Wang, J Wang… - Physical Chemistry …, 2023 - pubs.rsc.org
Developing a ligand with high affinity for a specific protein target is essential for drug design,
and water molecules are well known to play a key role in protein–drug recognition …
and water molecules are well known to play a key role in protein–drug recognition …
Protein–ligand complex solvation thermodynamics: Development, parameterization, and testing of GIST-based solvent functionals
T Hüfner-Wulsdorf, G Klebe - Journal of Chemical Information …, 2020 - ACS Publications
In drug design, the importance of molecular solvation and desolvation is increasingly
appreciated and water molecules are recognized as active contributors to protein–ligand …
appreciated and water molecules are recognized as active contributors to protein–ligand …
Investigation of structural analogs of hydroxychloroquine for SARS-CoV-2 main protease (Mpro): A computational drug discovery study
The main protease (Mpro) is the key enzyme of nCOVID-19 and plays a decisive role that
makes it an attractive drug target. Multiple analysis of crystal structures reveals the presence …
makes it an attractive drug target. Multiple analysis of crystal structures reveals the presence …